Dear Aashish,

I am not sure about AMBER, but what you are looking for is throughout possible with CHARMM.

You might look at their Internet portal CHARMMING:

https://www.charmming.org/charmming/

There is a possibility to properly formulate the task and even start the simulation to get the restart files and continue your work on your computers. CHARMM is possessed of the force field for chemically generalized consituents (not only bioorganic chemicals, but ).

Definitely, AMBER is also possessed of something like this, but it is not clear at least for me...

Respectfully yours,

Evgeni

Thank you sir

I definitely do this thing

The best approach would be to write a frcmod.* file that you can source in tleap.

You can find some sample frcmod files in your leap folder. The keyword you are looking for is NONBON, which is followed by a line defining the atom type and Lennard-Jones Parameter:

NONBON

Ag+ 1.212 0.3526418

(These are the Lennard-Jones parameter for Na+. Dont use these if you care for correctness.)

regards,

Martin

Thank you, sir, for your help

I have created Ag+ ion topology and inpcrd file in AMBER 16.